//Created by libAntimony v2.4
model Hinch__environment(time_)

  // Variable initializations:
  time_ = ;
end

model Hinch__cell_geometry(V_myo, V_SR, A_cap)

  // Variable initializations:
  V_myo = 25.84e3;
  V_SR = 2.098e3;
  A_cap = 1.534e4;
end

model Hinch__membrane(V, R, T, F, time_, FVRT, FVRT_Ca)

  // Assignment Rules:
  V := piecewise( 0 , ( geq(time_, 0)) && (time_ <= 200 ), -(80) );
  FVRT := (F * V) / (R * T);
  FVRT_Ca := 2 * FVRT;

  // Variable initializations:
  R = 8314.5;
  T = 295;
  F = 96487;
  time_ = ;
end

model Hinch__CaRU_Transitions(V, C_oc, C_co, Ca_i, alpha_p, alpha_m, beta_poc, beta_pcc, beta_m, epsilon_pco, epsilon_pcc, epsilon_m, mu_poc, mu_pcc, mu_moc, mu_mcc)

  // Assignment Rules:
  t_R := 1.17 * t_L;
  expVL := exp((V - V_L) / del_VL);
  alpha_p := expVL / (t_L * (expVL + 1));
  alpha_m := phi_L / t_L;
  beta_poc := power(C_oc, 2) / (t_R * (power(C_oc, 2) + power(K_RyR, 2)));
  beta_pcc := power(Ca_i, 2) / (t_R * (power(Ca_i, 2) + power(K_RyR, 2)));
  beta_m := phi_R / t_R;
  epsilon_pco := (C_co * (expVL + a)) / (tau_L * K_L * (expVL + 1));
  epsilon_pcc := (Ca_i * (expVL + a)) / (tau_L * K_L * (expVL + 1));
  epsilon_m := (b * (expVL + a)) / (tau_L * (b * expVL + a));
  mu_poc := (power(C_oc, 2) + c * power(K_RyR, 2)) / (tau_R * (power(C_oc, 2) + power(K_RyR, 2)));
  mu_pcc := (power(Ca_i, 2) + c * power(K_RyR, 2)) / (tau_R * (power(Ca_i, 2) + power(K_RyR, 2)));
  mu_moc := (theta_R * d * (power(C_oc, 2) + c * power(K_RyR, 2))) / (tau_R * (d * power(C_oc, 2) + c * power(K_RyR, 2)));
  mu_mcc := (theta_R * d * (power(Ca_i, 2) + c * power(K_RyR, 2))) / (tau_R * (d * power(Ca_i, 2) + c * power(K_RyR, 2)));

  // Variable initializations:
  V = ;
  C_oc = ;
  C_co = ;
  Ca_i = ;
  V_L = -2;
  del_VL = 7;
  phi_L = 2.35;
  t_L = 1;
  tau_L = 650;
  tau_R = 2.43;
  phi_R = 0.05;
  theta_R = 0.012;
  K_RyR = 41e-3;
  K_L = 0.22e-3;
  a = 0.0625;
  b = 14;
  c = 0.01;
  d = 100;
end

model Hinch__CaRU_states(alpha_p, alpha_m, beta_pcc, beta_poc, beta_m, y_oc, y_co, y_oo, y_cc, y_ci, y_oi, y_ic, y_io, y_ii)

  // Assignment Rules:
  denom := (alpha_p + alpha_m) * ((alpha_m + beta_m + beta_poc) * (beta_m + beta_pcc) + alpha_p * (beta_m + beta_poc));
  y_oc := (alpha_p * beta_m * (alpha_p + alpha_m + beta_m + beta_pcc)) / denom;
  y_co := (alpha_m * (beta_pcc * (alpha_m + beta_m + beta_poc) + beta_poc * alpha_p)) / denom;
  y_oo := (alpha_p * (beta_poc * (alpha_p + beta_m + beta_pcc) + beta_pcc * alpha_m)) / denom;
  y_cc := (alpha_m * beta_m * (alpha_m + alpha_p + beta_m + beta_poc)) / denom;
  y_ci := alpha_m / (alpha_p + alpha_m);
  y_oi := alpha_p / (alpha_p + alpha_m);
  y_ic := beta_m / (beta_pcc + beta_m);
  y_io := beta_pcc / (beta_pcc + beta_m);
  y_ii := (((((((1 - y_oc) - y_co) - y_oo) - y_cc) - y_ci) - y_ic) - y_oi) - y_io;

  // Variable initializations:
  alpha_p = ;
  alpha_m = ;
  beta_pcc = ;
  beta_poc = ;
  beta_m = ;
end

model Hinch__CaRU_reduced_states(y_oc, y_cc, y_co, alpha_p, alpha_m, beta_pcc, beta_m, epsilon_pco, epsilon_pcc, epsilon_m, mu_poc, mu_pcc, mu_moc, mu_mcc, r_1, r_2, r_3, r_4, r_5, r_6, r_7, r_8, z_1, z_2, z_3, z_4, time_)

  // Assignment Rules:
  r_1 := y_oc * mu_poc + y_cc * mu_pcc;
  r_2 := (alpha_p * mu_moc + alpha_m * mu_mcc) / (alpha_p + alpha_m);
  r_3 := (beta_m * mu_pcc) / (beta_m + beta_pcc);
  r_4 := mu_mcc;
  r_5 := y_co * epsilon_pco + y_cc * epsilon_pcc;
  r_6 := epsilon_m;
  r_7 := (alpha_m * epsilon_pcc) / (alpha_p + alpha_m);
  r_8 := epsilon_m;
  z_4 := ((1 - z_1) - z_2) - z_3;

  // Rate Rules:
  z_1' = -(r_1 + r_5) * z_1 + r_2 * z_2 + r_6 * z_3;
  z_2' = (r_1 * z_1 - (r_2 + r_7) * z_2) + r_8 * z_4;
  z_3' = (r_5 * z_1 - (r_6 + r_3) * z_3) + r_4 * z_4;

  // Variable initializations:
  y_oc = ;
  y_cc = ;
  y_co = ;
  alpha_p = ;
  alpha_m = ;
  beta_pcc = ;
  beta_m = ;
  epsilon_pco = ;
  epsilon_pcc = ;
  epsilon_m = ;
  mu_poc = ;
  mu_pcc = ;
  mu_moc = ;
  mu_mcc = ;
  z_1 = 0.98859;
  z_2 = 0.0087302;
  z_3 = 0.0026566;
  time_ = ;
end

model Hinch__DS_Calcium_Concentrations(Ca_i, Ca_SR, Ca_o, FVRT_Ca, g_D, J_R, J_L, C_cc, C_oc, C_co, C_oo)

  // Assignment Rules:
  C_cc := Ca_i;
  C_oc := piecewise( (Ca_i + ((J_L / g_D) * Ca_o * FVRT_Ca * exp(- FVRT_Ca)) / (1 - exp(- FVRT_Ca))) / (1 + ((J_L / g_D) * FVRT_Ca) / (1 - exp(- FVRT_Ca))) , abs(FVRT_Ca) > 0.000000001 , (Ca_i + (J_L / g_D) * Ca_o) / (1 + J_L / g_D) );
  C_co := (Ca_i + (J_R / g_D) * Ca_SR) / (1 + J_R / g_D);
  C_oo := piecewise( (Ca_i + (J_R / g_D) * Ca_SR + ((J_L / g_D) * Ca_o * FVRT_Ca * exp(- FVRT_Ca)) / (1 - exp(- FVRT_Ca))) / (1 + J_R / g_D + ((J_L / g_D) * FVRT_Ca) / (1 - exp(- FVRT_Ca))) , abs(FVRT_Ca) > 0.000000001 , (Ca_i + (J_R / g_D) * Ca_SR + (J_L / g_D) * Ca_o) / (1 + J_R / g_D + J_L / g_D) );

  // Variable initializations:
  Ca_i = ;
  Ca_SR = ;
  Ca_o = ;
  FVRT_Ca = ;
  g_D = ;
  J_R = ;
  J_L = ;
end

model Hinch__LCC_and_RyR_fluxes(g_D, J_R, J_L, Ca_i, Ca_SR, Ca_o, FVRT_Ca, J_Loo, J_Loc, J_Rco, J_Roo)

  // Assignment Rules:
  J_Loo := piecewise( (((J_L * FVRT_Ca) / (1 - exp(- FVRT_Ca))) * ((Ca_o * exp(- FVRT_Ca) - Ca_i) + (J_R / g_D) * (Ca_o * exp(- FVRT_Ca) - Ca_SR))) / (1 + J_R / g_D + ((J_L / g_D) * FVRT_Ca) / (1 - exp(FVRT_Ca))) , abs(FVRT_Ca) > 0.00001 , (((J_L * 0.00001) / (1 - exp(-(0.00001)))) * ((Ca_o * exp(-(0.00001)) - Ca_i) + (J_R / g_D) * (Ca_o * exp(-(0.00001)) - Ca_SR))) / (1 + J_R / g_D + ((J_L / g_D) * 0.00001) / (1 - exp(-(0.00001)))) );
  J_Loc := piecewise( (((J_L * FVRT_Ca) / (1 - exp(- FVRT_Ca))) * (Ca_o * exp(- FVRT_Ca) - Ca_i)) / (1 + ((J_L / g_D) * FVRT_Ca) / (1 - exp(- FVRT_Ca))) , abs(FVRT_Ca) > 0.00001 , (((J_L * 0.00001) / (1 - exp(-(0.00001)))) * (Ca_o * exp(-(0.00001)) - Ca_i)) / (1 + ((J_L / g_D) * 0.00001) / (1 - exp(-(0.00001)))) );
  J_Rco := (J_R * (Ca_SR - Ca_i)) / (1 + J_R / g_D);
  J_Roo := piecewise( (J_R * ((Ca_SR - Ca_i) + (((J_L / g_D) * FVRT_Ca) / (1 - exp(- FVRT_Ca))) * (Ca_SR - Ca_o * exp(- FVRT_Ca)))) / (1 + J_R / g_D + ((J_L / g_D) * FVRT_Ca) / (1 - exp(- FVRT_Ca))) , abs(FVRT_Ca) > 0.00001 , (J_R * ((Ca_SR - Ca_i) + (((J_L / g_D) * 0.00001) / (1 - exp(-(0.00001)))) * (Ca_SR - Ca_o * exp(-(0.00001))))) / (1 + J_R / g_D + ((J_L / g_D) * 0.00001) / (1 - exp(-(0.00001)))) );

  // Variable initializations:
  g_D = ;
  J_R = ;
  J_L = ;
  Ca_i = ;
  Ca_SR = ;
  Ca_o = ;
  FVRT_Ca = ;
end

model Hinch__RyR_current(y_oo, y_co, y_oc, beta_pcc, beta_m, J_Roo, J_Rco, z_1, z_3, V_myo, N, J_R1, J_R3, I_RyR)

  // Assignment Rules:
  J_R1 := y_oo * J_Roo + J_Rco * y_co;
  J_R3 := (J_Rco * beta_pcc) / (beta_m + beta_pcc);
  I_RyR := ((z_1 * J_R1 + z_3 * J_R3) * N) / V_myo;

  // Variable initializations:
  y_oo = ;
  y_co = ;
  y_oc = ;
  beta_pcc = ;
  beta_m = ;
  J_Roo = ;
  J_Rco = ;
  z_1 = ;
  z_3 = ;
  V_myo = ;
  N = ;
end

model Hinch__LCC_current(y_oo, y_oc, alpha_p, alpha_m, J_Loo, J_Loc, z_1, z_2, V_myo, N, J_L1, J_L2, I_LCC)

  // Assignment Rules:
  J_L1 := J_Loo * y_oo + J_Loc * y_oc;
  J_L2 := (J_Loc * alpha_p) / (alpha_p + alpha_m);
  I_LCC := ((z_1 * J_L1 + z_2 * J_L2) * N) / V_myo;

  // Variable initializations:
  y_oo = ;
  y_oc = ;
  alpha_p = ;
  alpha_m = ;
  J_Loo = ;
  J_Loc = ;
  z_1 = ;
  z_2 = ;
  V_myo = ;
  N = ;
end

model Hinch__CaRU(g_D, J_R, J_L, V_myo, N, V, Ca_i, Ca_o, Ca_SR, time_, FVRT_Ca, I_RyR, I_LCC)

  // Sub-modules, and any changes to those submodules:
  CaRU_Transitions: Hinch__CaRU_Transitions(V, C_oc, C_co, Ca_i, alpha_p, alpha_m, beta_poc, beta_pcc, beta_m, epsilon_pco, epsilon_pcc, epsilon_m, mu_poc, mu_pcc, mu_moc, mu_mcc);
  CaRU_states: Hinch__CaRU_states(alpha_p, alpha_m, beta_pcc, beta_poc, beta_m, y_oc, y_co, y_oo, y_cc, y_ci, y_oi, y_ic, y_io, y_ii);
  CaRU_reduced_states: Hinch__CaRU_reduced_states(y_oc, y_cc, y_co, alpha_p, alpha_m, beta_pcc, beta_m, epsilon_pco, epsilon_pcc, epsilon_m, mu_poc, mu_pcc, mu_moc, mu_mcc, r_1, r_2, r_3, r_4, r_5, r_6, r_7, r_8, z_1, z_2, z_3, z_4, time_);
  DS_Calcium_Concentrations: Hinch__DS_Calcium_Concentrations(Ca_i, Ca_SR, Ca_o, FVRT_Ca, g_D, J_R, J_L, C_cc, C_oc, C_co, C_oo);
  LCC_and_RyR_fluxes: Hinch__LCC_and_RyR_fluxes(g_D, J_R, J_L, Ca_i, Ca_SR, Ca_o, FVRT_Ca, J_Loo, J_Loc, J_Rco, J_Roo);
  RyR_current: Hinch__RyR_current(y_oo, y_co, y_oc, beta_pcc, beta_m, J_Roo, J_Rco, z_1, z_3, V_myo, N, J_R1, J_R3, I_RyR);
  LCC_current: Hinch__LCC_current(y_oo, y_oc, alpha_p, alpha_m, J_Loo, J_Loc, z_1, z_2, V_myo, N, J_L1, J_L2, I_LCC);

  // Variable initializations:
  g_D = 0.065;
  J_R = 0.02;
  J_L = 9.13e-4;
  N = 50000;
end

model Hinch__Na_Ca_Exchanger(FVRT, Na_i, Na_o, Ca_i, Ca_o, I_NaCa)

  // Assignment Rules:
  I_NaCa := (g_NCX * (exp(eta * FVRT) * power(Na_i, 3) * Ca_o - exp((eta - 1) * FVRT) * power(Na_o, 3) * Ca_i)) / ((power(Na_o, 3) + power(K_mNa, 3)) * (Ca_o + K_mCa) * (1 + k_sat * exp((eta - 1) * FVRT)));

  // Variable initializations:
  FVRT = ;
  K_mNa = 87.5;
  K_mCa = 1.38;
  eta = 0.35;
  k_sat = 0.1;
  g_NCX = 38.5e-3;
  Na_i = ;
  Na_o = ;
  Ca_i = ;
  Ca_o = ;
end

model Hinch__SERCA(I_SERCA, Ca_i)

  // Assignment Rules:
  I_SERCA := (g_SERCA * power(Ca_i, 2)) / (power(K_SERCA, 2) + power(Ca_i, 2));

  // Variable initializations:
  g_SERCA = 0.45e-3;
  K_SERCA = 0.5e-3;
  Ca_i = ;
end

model Hinch__Sarcolemmal_Ca_pump(Ca_i, I_pCa)

  // Assignment Rules:
  I_pCa := (g_pCa * Ca_i) / (K_mpCa + Ca_i);

  // Variable initializations:
  g_pCa = 0.0035e-3;
  K_mpCa = 0.5e-3;
  Ca_i = ;
end

model Hinch__Background_Ca_current(V, R, T, F, Ca_i, Ca_o, E_Ca, I_CaB)

  // Assignment Rules:
  E_Ca := ((R * T) / (2 * F)) * ln(Ca_o / Ca_i);
  I_CaB := g_CaB * (E_Ca - V);

  // Variable initializations:
  V = ;
  R = ;
  T = ;
  F = ;
  Ca_i = ;
  Ca_o = ;
  g_CaB = 2.6875e-8;
end

model Hinch__SR_Ca_leak_current(Ca_i, Ca_SR, I_SR)

  // Assignment Rules:
  I_SR := g_SRl * (Ca_SR - Ca_i);

  // Variable initializations:
  Ca_i = ;
  Ca_SR = ;
  g_SRl = 1.8951e-5;
end

model Hinch__troponin_Ca_buffer(TRPN, Ca_i, I_TRPN)

  // Assignment Rules:
  I_TRPN := k_m_TRPN * (B_TRPN - TRPN) - k_p_TRPN * TRPN * Ca_i;

  // Variable initializations:
  k_m_TRPN = 0.04;
  k_p_TRPN = 0.04e3;
  B_TRPN = 70e-3;
  TRPN = ;
  Ca_i = ;
end

model Hinch__calmodulin_Ca_buffer(Ca_i, beta_CMDN)

  // Assignment Rules:
  beta_CMDN := power(1 + (k_CMDN * B_CMDN) / power(k_CMDN + Ca_i, 2), -(1));

  // Variable initializations:
  k_CMDN = 2.382e-3;
  B_CMDN = 50e-3;
  Ca_i = ;
end

model Hinch__intracellular_ion_concentrations(Na_i, Ca_i, Ca_SR, TRPN, time_, V_myo, V_SR, beta_CMDN, I_SERCA, I_pCa, I_CaB, I_TRPN, I_SR, I_NaCa, I_RyR, I_LCC)

  // Assignment Rules:
  CaSR_plot := (Ca_SR * V_SR) / V_myo;

  // Rate Rules:
  Ca_i' = beta_CMDN * (((((I_LCC + I_RyR) - I_SERCA) + I_SR + I_NaCa) - I_pCa) + I_CaB + I_TRPN);
  Ca_SR' = (V_myo / V_SR) * ((- I_RyR + I_SERCA) - I_SR);
  TRPN' = I_TRPN;

  // Variable initializations:
  Na_i = 10;
  Ca_i = 0.0001;
  Ca_SR = 700e-3;
  TRPN = 0.0636364;
  time_ = ;
  V_myo = ;
  V_SR = ;
  beta_CMDN = ;
  I_SERCA = ;
  I_pCa = ;
  I_CaB = ;
  I_TRPN = ;
  I_SR = ;
  I_NaCa = ;
  I_RyR = ;
  I_LCC = ;
end

model Hinch__extracellular_ion_concentrations(Na_o, Ca_o)

  // Variable initializations:
  Na_o = 140;
  Ca_o = 1;
end

model *Hinch____main()

  // Sub-modules, and any changes to those submodules:
  environment: Hinch__environment(time_);
  cell_geometry: Hinch__cell_geometry(V_myo, V_SR, A_cap);
  membrane: Hinch__membrane(V, R, T, F, time_, FVRT, FVRT_Ca);
  CaRU: Hinch__CaRU(g_D, J_R, J_L, V_myo, N, V, Ca_i, Ca_o, Ca_SR, time_, FVRT_Ca, I_RyR, I_LCC);
  Na_Ca_Exchanger: Hinch__Na_Ca_Exchanger(FVRT, Na_i, Na_o, Ca_i, Ca_o, I_NaCa);
  SERCA: Hinch__SERCA(I_SERCA, Ca_i);
  Sarcolemmal_Ca_pump: Hinch__Sarcolemmal_Ca_pump(Ca_i, I_pCa);
  Background_Ca_current: Hinch__Background_Ca_current(V, R, T, F, Ca_i, Ca_o, E_Ca, I_CaB);
  SR_Ca_leak_current: Hinch__SR_Ca_leak_current(Ca_i, Ca_SR, I_SR);
  troponin_Ca_buffer: Hinch__troponin_Ca_buffer(TRPN, Ca_i, I_TRPN);
  calmodulin_Ca_buffer: Hinch__calmodulin_Ca_buffer(Ca_i, beta_CMDN);
  intracellular_ion_concentrations: Hinch__intracellular_ion_concentrations(Na_i, Ca_i, Ca_SR, TRPN, time_, V_myo, V_SR, beta_CMDN, I_SERCA, I_pCa, I_CaB, I_TRPN, I_SR, I_NaCa, I_RyR, I_LCC);
  extracellular_ion_concentrations: Hinch__extracellular_ion_concentrations(Na_o, Ca_o);
end